MolNFT v1 · #164001 · protein
Methyltransferase mtga from desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)
6SK4 · METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase: “Methyltransferase mtga from desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)”. X-ray diffraction, 1 ligand (THH), 11 pockets (best druggability 0.71).…
- PDB
- 6SK4
- Type
- protein
- Length
- 1,197 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q24SP6
- Ligands
- THH
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase (EC 2.1.1.-) | protein | 299 | 45% helix, 19% strand | Q24SP6 |
| B | METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase (EC 2.1.1.-) | protein | 296 | 45% helix, 18% strand | Q24SP6 |
| C | METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase (EC 2.1.1.-) | protein | 298 | 44% helix, 19% strand | Q24SP6 |
| D | METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase (EC 2.1.1.-) | protein | 304 | 46% helix, 18% strand | Q24SP6 |
Ligands and binding sites
- THH · N-[4-({[(6S)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.71 | 0.76 | 73 | THH, GOL |
| 2 | 370 | 0.60 | 0.77 | 38 | empty |
| 3 | 294 | 0.59 | 0.78 | 37 | empty |
| 4 | 315 | 0.59 | 0.77 | 33 | THH |
| 5 | 344 | 0.59 | 0.76 | 40 | THH |
Interfaces
5 interfaces between chains.
- C–D · 1910 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1908 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 142 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 120 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6SK4 · Methyltransferase MtgA from Desulfitobacterium hafniense in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q24SP6 · AlphaFold monomer V2.0 prediction for METHYLCORRINOID:TETRAHYDROFOLATE methyltransferase… · a predicted model of the same protein · chain C against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q24SP6
- Elsewhere: RCSB PDB 6SK4 · PDBe 6SK4 · UniProt Q24SP6
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